I hope that the article that Jennifer has provided helped answer most of your questions on how to change your subdomain! I have gone through each of your questions to verify that they have been addressed and explained in the documentation above. As you can see, there are a lot of things involved with making the switch, but we will help you along to make this as seamless as possible.

Having JIRA installed on your account does add a level of complication, but if you follow the guidelines below, it should be relatively seamless as well:

When getting ready to make the subdomain change, please make sure that your are logged into Zendesk as a Admin, and in Jira as someone who is able to install Add-ons.

How does this work if I am changing from JIRA cloud to JIRA server. The ticket numbers all stay the same but the domain will change from xxxxxx.atlassian.net to customer.url.com for example....is there a ways to not lose all my linked tickets?

The process to move your linked tickets across to your new URL is to raise a ticket with us and schedule in a time for our JIRA developers to conduct a cutover. Be sure to include your your old and new JIRA URL in the ticket. During this cutover, any linked tickets during this time will not be pushed through. Hope this helps!